Growing
by Mandie scifi lover
Summary: Has anyone noticed how much Weir and John fight in season 1? This story assumes they are married but have been seperated for a couple weeks before the mission leaves. Planning on adding scenes through season 1. Completely original scenes- no use of episode text.
1. Chapter 1

John entered their house quietly. The door to their apartment squeaked a little as he closed it, causing him to flinch slightly. Tossing his keys on the table next to the door, he shrugged off his coat and made his way into the kitchen, intent on making some decaf before he went to bed. When he rounded the corner into their kitchen, the table came into view and he stopped in his tracks. It was covered with dishes, food heaped on them, two obviously burned candles in the middle of the table. There was a box setting next to one of the plates. The plate had been intended for him; it had a small glass of Jack Daniels setting in front of it.

His heart sinking, he made his heavy legs move forward so he could pick up the box. Opening it, he found a long silver chair and a note that read: "Happy seven years! I know you don't like to wear your ring on missions so I hope you'll wear it on this chain. Lots of love, E."

Sighing deeply, he set the box down again and turned to go into the other room but found Elizabeth standing in the door way, her face blotchy, her eyes bloodshot. He could barely meet her eyes.

"'Lizabeth…" he started uncomfortably.

"No," she cut him off. "John, I don't want to hear another excuse. We've talked about this so many times!" As she said the words, her voice broke and she took a breath, trying not to cry. Looking into her eyes, he couldn't even apologize.

"I…" she began again. "John, I wanted this to work! I _want _this to work! But you're just not _here_! And I don't just mean physically, I mean emotionally, and relationally! Every time we talk about it, you say it's going to be different but it never is!" She wiped her tears away angrily amid a noise of disgust.

"Hey," John began, "I'm not exactly the _only _one to blame here."

"Really?" Elizabeth's eyes spit fire. "You honestly believe that? Because I'm _trying_! I'm trying to make this work! And even with all my experience negotiating and making people work together, I _can't _make us work together! I can't make _you_ work with me!"

"Hey," John said as he moved towards her. "I haven't been the one _complaining _constantly about _stupid _things that I think need to be changed! I'm not the one who's been _constantly _nagging you about your actions and what I _need _from you! I'm the one who's been trying to _change _things, instead of complain about them!"

"You think I'm complaining? You think the things I'm telling you are _stupid_? JOHN, you missed our SEVEN YEAR ANNIVERSARY! I bought you a THOUGHTFUL GIFT! Did you even THINK of buying me something? Did you even REMEMBER it was today?"

John could feel his anger starting to spiral so he tried to take a breath. "Elizabeth, I've been a _little _busy WORKING. I was on assignment and I got held up on my way back. I was a little late coming home and I'm SORRY about that."

Elizabeth was shaking her head as he was talking. "No, John, no you don't even SEE IT! Don't you understand how much these things MATTER to me? I NEED you! I need you to show me you love me! And when you forget our anniversary, that makes me feel like you don't LOVE ME ANYMORE!"

Tears started to come down again as she continued, "And I'm sick of feeling that way John! I'm sick of feeling unloved. I'm sick of feeling like your work is more important than me!"

John growled as he turned away from her, putting his fist down on the table a little more firmly than he had intended. "And _I'm_ sick of _you_ nagging me about everything I do!" He turned to her again. "I'm sick of feeling like every action of mine is under scrutiny. I'm sick of worrying about what your reaction's going to be when I get home! And I'm SORRY about tonight, I was preoccupied!"

Elizabeth's face contorted into a harsh laugh. "Preoccupied? You know I turned down a negotiation for this anniversary! I decided specifically to take off today so we could be together and have a nice meal but obviously it wasn't important enough to you!"

John's gray eyes flashed and his gaze tore into Elizabeth. "Fine, you know what, you're so damn determined to believe I forgot on purpose, there's nothing I can say that will change your mind. So FINE, I didn't come home because it wasn't important! I didn't come home because I DON'T LOVE YOU! I didn't come home because I don't ENJOY BEING WITH YOU! IS THAT WHAT YOU WANT TO HEAR?"

After the words had left his mouth, he felt a knife enter his gut. He had gone too far. Tears began streaming down her face and she looked down, twirling the ring on her finger, tears dripping onto the floor. John held his breath for a moment and then took a step forward, touching her lightly on the arm. As he did, she shoved him away angrily and he retreated a couple steps. Looking him in the eyes, her face contorted, she said,

"John, I think it would be best if I move out for a while."

With that, she left the kitchen and he could hear her banging around their room, packing her suitcase. He didn't move from the position he was standing in until the slamming door broke him out of his revere. Then, he went to the table, carefully took the necklace from its box, slid his ring on the chain, and put it around his neck to hang with his dog tags.

He sat there for a long time.

OOOOO

They had been living apart for three weeks when John made his appearance at the Antarctic base. It caught Weir almost entirely by surprise; to see him sitting there in the chair, the solar system map spread out above his head, the technology coming effortlessly to life under his touch. She had to admit he looked good; hot was the right word. She never could resist him in his uniform, especially with his hair mussed from the helmet.

Still on the high from discovering Atlantis was a real place, she was delusional enough to think John would agree to come to Atlantis with her. She should have been more realistic.

"John!" she called to him across the floor after they had finished with the chair. He looked at her with surprised gray eyes and gave her a small nod as she made her way over to him.

"Elizabeth. I see this is the top secret project you've been working on."

Elizabeth had to smile at that. Her top secret projects had been the subject of innumerable jokes and fights over the past couple months.

"Yes, well, it's pretty amazing stuff." She paused for a moment, allowing herself to smile at him. "And… that's kind of what I want to talk to you about."

He frowned at her and crossed his arms. "What? Me coming to work in Antarctica? My own secret projects?"

She shook her head. "No. Have you been briefed about Atlantis?"

He shrugged. "Sort of, for all of five minutes."

Letting out a breath, she connected eyes with him again. "I want you to come along."

The silence reigned for a long time. John stared at her hard for a good thirty seconds before looking away. After that, he looked to the side and began to fidget slightly with his flight suit.

" 'Lizabeth, I don't know if it's such a good idea for me to be part of leadership on Atlantis, what with our relationship _issues_ and all."

She frowned. "John, this isn't just about you and me. I'm not asking for selfish reasons. I want you there because the expedition needs you. You can work the Ancient technology like a natural and we don't have anyone on the team yet who can do that."

John looked intently at the ice packed wall to his left and nodded his head slightly. Of course, it _would_ be about what's best for the team and not what's best for them. That was so Elizabeth. After a moment he turned and his face was set. "All right, my answer is no."

She started to protest but he held up a hand to forestall any further arguments. "Elizabeth, I'm really not in the mood to get into another fight with you. My answer is no. I'm sorry."

Without another word, he made his way towards the elevator. Watching him walk away, Elizabeth knew she couldn't let him go. Besides the fact that he was invaluable to the expedition, she just wasn't ready to give up on him yet. She still loved him. Maybe a change of scenery would do them some good. And she was pretty sure General O'Neill could convince him to come.


	2. Chapter 2

John almost died today.

It was a thought that played unbidden on repeat in her head. They had shocked him with a defibrillator in the hopes of saving his life and it had almost killed him. Not to mention the huge alien bug that had attached itself to his neck.

There had been a moment when she thought he was a goner. She remembered him wanting to say his last words, and her reluctance to hear them. In that moment, the regret she felt for the state of their relationship was almost too much to bear.

But, he was still alive. And now she wondered what he had been about to say. She was smart enough to realize he wasn't going to say, "take care of each other" like he pretended. But she did wonder what he had been thinking in that moment.

He was released from the infirmary the next day and Elizabeth made a bee line for his room. Carson had informed her that he had been released on the condition that he remain close to his room and avoid intense physical activity, at least until Carson was sure there were no remaining effects.

When she got to his room, she felt her heart beating wildly in her chest and she shook her head at herself. She felt like the young girl she'd been when they met. He was a cocky flyboy and she was a brainiac law student who was looking for some fun in her life. Things had changed so much since then.

Without another though, she rang the bell to John's door and tried to still her heart. She heard him rustling within, heard a muffled "just a minute!" and then John was at the door, dark gray swets and his go-to black t-shirt covering his body. Seeing him up and about almost made tears come to Elizabeth's eyes and before she had the chance to think about it, she had him wrapped up in a hug, her face buried in his neck. He was a little shocked but his arms came around her after a moment and held her close.

Soon, he pulled her back into his room, closing the door, and pried her arms off him. Still holding her hands, he looked into her eyes.

"Hey, I'm fine. I'm not going anywhere. Carson's the best doctor anywhere. He wasn't going to let me die."

Her eyes welled with tears and she blinked rapidly. "Oh John, it doesn't matter how good a doctor he is… When you were on the jumper, and you were… trying to say your last thoughts I… I just had so many regrets about where we are now!"

She looked at him deeply and then pulled her hands away, moving to pace around the room, her arms tight around her body. John remained by the door, a little shocked at her reaction.

"John," Elizabeth continued, "I… I don't want us to be alienated! I don't want to miss you every night. I don't want to fight with you. I want us to love each other and be together!"

They looked at each other across the room, Elizabeth with tears brimming in her eyes. John took a deep breath and it came out shakier than he had expected.

"I wish…" Elizabeth halted. "I wish we could find that passion we had when we met each other and we were young and you thought you were invincible and I… I thought you could do no wrong."

John gave her a sad smile. "You know it will never be that way."

Smiling a little, Elizabeth nodded. "I know. We're not young anymore. But… I want to be with you John. I don't want to lose you."

He looked at her from across the room, saw the sincerity in her eyes, and couldn't deny that he felt the same way. Yes, they fought a lot, and yes sometimes it hurt like hell to be with her, but he wanted her more than he didn't want those things. Of course, a big part of that feeling was probably due to the fact that he wanted her physically but, his mind wasn't thinking very clearly at the moment.

Walking over to her, he stopped right in front of her; looking at her beautiful face, her bright eyes. Taking one hand, he ran it through her auburn hair, felt her respond to his touch. He let his eyes slide over her body and then back to her face, connecting with her eyes. Snaking a hand around her waist, he felt the outline of her hip; let his hand creep upward to her back. Then, slowly, he connected lips with hers, feeling their soft warmth on his, hearing her breath increase in response.

He deepened the kiss quickly and felt her arms come around his body. It had been too long since they'd been together and he could tell she felt the same way. Pushing her back gently, he pinned her against the wall and felt her groan lightly in response to the weight of his body. Kissing her more intensely, he felt her hands push under his shirt. He broke away to look into her eyes once more, tracing one hand over her face.

"I love you Elizabeth."

She smiled. "I love you too."

OOOOO

The next morning, neither John nor Elizabeth felt regret at what had happened the night before. Elizabeth woke feeling more rested than she had in a long time. They decided to go for breakfast together before facing the day and found it quite enjoyable. Elizabeth was trying not to allow herself to hope, but it was hard when things were going so well. She should have known it wouldn't last.

Though they had a good time at breakfast, and were able to have an enjoyable conversation without fighting, they could both feel the tension hanging in the air. It was like their relationship was a Jenga tower that had been piled too high; ready to fall at any moment. They both knew it wouldn't take much to break the tenuous peace between them… and they were right.


	3. Chapter 3

Chapter 3

"We need to talk, now," John said, his eyes flashing. Elizabeth nodded curtly at him, watching Lt. Ford being rolled away on the gurney. John's emotions barely under control, he started up to Elizabeth's office without waiting for her, taking the stairs two at a time.

She had almost killed Ford and Teyla. If she hadn't lowered the shield when she did, they would have been dead or captured by the wraith. What she was thinking, he had no idea. And her mistrust of Teyla was ridiculous; hadn't Teyla done enough already to earn her trust?

Arriving at her office, he tapped his finger on her desk as he watched her walk over the bridge and motion the door shut behind her.

"What?" she asked, her arms crossed over her chest.

"_What_?" he asked incredulously. "You almost _killed _Ford and Teyla. If you hadn't lowered the shield-

"But I _did_ Major," she cut him off, using his designation to annoy him. He pressed his lips together.

"Hasn't Teyla done enough to earn your trust? Hasn't she-

"Do you have another explanation? A better one?" she cut him off again. "Because Bates is right, Teyla was the only Athosian who knew about that mission, and her disappearance is more than a little suspicious. The only other option is that it was one of our own people. I don't believe _that _for a minute, what about you?"

His eyes flashing, he stared her down. "Teyla is a trustworthy person. She's proven herself to be loyal and truthful. Now, suddenly, because we don't have any other logical option we suspect her? How is that fair?"

"John, you're letting your personal feelings for her cloud your judgment! I know she's a beautiful woman but _come on_! You're the military commander of this city! You can't let your _feelings _affect how you act!"

John swallowed hard and took a breath to keep from exploding. "What _exactly _are you saying, _Elizabeth_?"

She stared at him for a long moment, her gaze never wavering. "I'm saying that I see how you look at her. Ever since we met her you've been smitten. You know I'm not usually a jealous person, unlike _someone_ I know, but this is going a little far don't you think?"

John took a step towards her. "I'm not blind Elizabeth. Teyla is a very beautiful woman. I'm sorry if it _bothers_ you that I notice that."

Elizabeth clenched her jaw. "But you don't just look at her do you? It's more than that."

He looked at her with an incredulous expression. "Are you saying you think I'm _with _her? You think I'm married to you but seeing Teyla on the _side_?"

Elizabeth pressed her lips together and stared at him.

Pulling back a little, John stared back. "Who the HELL do you think I am? You obviously don't know me as well as I thought. Elizabeth, I would NEVER cheat on you, and the fact that you think I would is probably the biggest INSULT you could ever give me."

"FINE," Elizabeth ground out, "then why can't you see how likely it is that Teyla is the one who is giving us away to the wraith?" Her voice was deadly quiet and he could see her working to keep the tension from exploding out of her body. Walking towards her, he stopped one step away.

"You're the one who can't see that Teyla is innocent. You're so worried that I'm having an affair with her, you can't see the reality. Teyla is a good person and she would NEVER betray us to the wraith. And the fact that you think I would have an affair in the first place?" He shook his head. "I can't see a future in a relationship that lacks that much trust."

With one last hard look at her, he left her office.

OOOOO

She had been innocent the whole time.

Teyla had no idea she was giving away her teams position to the wraith. Elizabeth had already apologized to Teyla and she had been very gracious. The Athosians movement to the main land had been a tension easer between everyone and Weir had hope that their continued relationship would be on better terms. Still, she had one person to apologize to that she didn't think would be as forgiving.

Walking down the hall slowly, she continued to work on her computer, hoping to avoid the dreaded confrontation as long as possible. Because she was looking down, she almost plowed straight into John, who was just crossing the corridor.

Looking up startled, Elizabeth had to smile a little, though it came out something like a grimace. "John! Where are you headed?"

He looked at her for a moment and then shrugged. "My room. Just coming from the brig."

They looked at each other for a long moment and then John broke the silence. "Look, it's been a long day so, I'll see you tomorrow."

Without waiting for her response, he started down the corridor. Elizabeth jogged to catch up.

"John, wait." She laid a light hand on his arm and looked into his eyes as he turned. Sighing a little, she said, "I'm sorry, really and truly. I didn't know what was going on and my first priority is protecting this city. All evidence was pointing to Teyla and I took the necessary precautions." She paused as she watched his jaw work in evident anger.

"John," she continued, "I already apologized to Teyla and she was surprisingly… accepting. I don't think it will get in the way of her and my relationship moving forward."

John looked away from her, nodded curtly, and then continued walking down the hall. Elizabeth watched him go for a moment and then sighed, jogging after him again. Turing around him, she placed a hand on his chest.

"Stop." Her eyes were pleading. "John, I know that I accused you wrongly and I'm sorry for that. I really am. You were right. Teyla is a good person and I trust her. But, she doesn't know we're married and John, take it from another woman, she's attracted to you. Since we've been separated things have been different between us and I don't want to lose you to someone else." She let her hand drop when she finished and watched his eyes.

He sighed and then rubbed his head with his hand. "Look, Elizabeth, we may have rushed back into things a little. I'm… I'm not ready to be back together and after today, I think it's pretty clear you're not either."

Elizabeth, a little surprised, allowed her face to fall. Stepping back, she nodded curtly. "All right, if that's what you want."

John sighed. "I'm sorry."

He made his way down the hall, rounding a corner soon after, and leaving a very down Elizabeth in his wake.


	4. Chapter 4

A couple days later, John went to the main land to visit Teyla. As much as he didn't want to admit it to himself, Elizabeth had been right about two things: Teyla was attracted to him and he needed to tell her they were married.

He radioed ahead to see if it was all right for him to come. Teyla sounded down right excited he was visiting and he grimaced thinking of what he needed to tell her. Now that Elizabeth had made him realize there was an attraction between him and Teyla, he noticed it a lot more than he had before.

On his way over, he rehearsed what he was going to say, every time rejecting the words. They either sounded stupid or lame or just plain insincere. He didn't know how he was going to start the conversation, since he and Teyla really had no reason to talk about it, and he didn't want to make Teyla uncomfortable.

John knew that while he was with Elizabeth, he couldn't be with anyone else, but he had to admit he was tempted to see what would happen between him and Teyla. Of course, Teyla would never be okay with it if she knew he was married, and she would probably lose all respect for him if he kept that fact from her. That fact more than anything else kept his thoughts and temptations in check.

Sighing as he put down the jumper, he felt the odd sensation of butterflies in his stomach. Ignoring them resolutely, he opened the hatch and saw Teyla's face smiling at him from below. Walking down the ramp, she surprised him by greeting him with a hug. She must have picked up on that particular greeting by observing the other members of the Atlantis mission. He awkwardly put his arms around her also and then she broke away.

"Major, it is good to see you." Her face was smiling.

He nodded and smiled back, a little hesitantly. "Yeah, you too. You're people settling in okay?"

She nodded and gestured that he should follow. "Yes, they are. We are finding this land to be a very suitable place for us to live. Though it is not home, it may be one day."

They walked through the camp and Teyla showed him many of the things they had built since they'd arrived. She also introduced him to several people he had not yet met. When they had made their way through the whole village, Teyla turned to him.

"John, I would like to show you a beautiful place I have discovered. It is a short walk from here, if you are up for it?"

John raised his eyebrows in interest and nodded. "Sure, I'm always up for a walk."

They made their way through the woods for a time until the woods cleared to reveal a beautiful, steep cliff face and a wide expanse of sparkling water.

"Wow," John commented, "That is beautiful."

Teyla nodded and smiled, sitting down on the ground near the edge. "Yes, it is."

John sat down next to her, taking a deep breath and knowing this was the moment he needed to tell her. Turning his face, he looked at her, taking in her brown skin and beautiful dark hair, so different from Elizabeth. She turned to look at him a moment later and gave him a shy smile. He cleared his throat, trying to remember what he was going to say. She beat him to it.

"John," she started. She seemed to wrestle with herself for a moment as she looked at him but then, she put a hand out to touch his face and pulled him into a kiss.

Despite himself, John felt tingles course through his body at the feel of her soft lips. It was so different from Elizabeth. It had been so long since he'd been with anyone else he forgot what it felt like. But, suddenly, he felt his gut clench and a sour taste enter his mouth. What was he thinking? He couldn't do this to Elizabeth, even if they were separated. He wasn't ready to be done trying to work things out.

Quickly, he pushed Teyla away with a hand, grimacing as he did. He looked at her confused face and took a breath.

"I'm sorry Teyla, I… I shouldn't have let you do that."

"Am I unpleasing to you?" she asked, her expression still confused.

John started to laugh but held it back. "No, no not at all. It's not that. You're beautiful." He sighed as he looked at her and then turned to look at the ocean.

"Teyla, your people have marriage right? Like when two people love each other and agree to be together forever?"

"Yes, life mates, of course we do. Why?"

John sighed. "Teyla, I'm… I'm married to Dr. Weir." He turned to look at her again and saw her expression of confusion become one of anger as well.

"Your life mate is Dr. Weir and you did not tell me?" Her eyes flashed at him.

"Oh, come on Teyla, I had no reason to tell you! And we're not even sure if we're going to _stay _married."

She frowned. "You do not know if you are going to stay with your life mate for life?"

John looked away, a little angry, and tried to collect his thoughts. "Look Teyla, on Earth, life mates don't always stay life mates. If two people stop getting along or stop loving each other, then they split up. Dr. Weir and I fight a lot and we don't know if we want to stay together."

Teyla turned her brown eyes to look over the water, thinking about what he'd said. "But, is not a life mate for life? Is that not the point of the union?"

John let out a grunt of frustration. "Maybe among your people it IS for life, but among people from Earth, sometimes it's not."

"But, you were not sure of your life bonding and yet you still chose to come to Atlantis together? To _lead _Atlantis together? Do you think that was wise?"

"Well," John said, sarcasm heavy in his voice, "It was either that or never see each other again. I think neither of us was willing to be completely done."

There was silence for a time as they looked at the water. Teyla was the one who broke it.

"Do you still love her?"

John shrugged. "Honestly, I don't know. I think I do but almost every time we're together we find something new to fight about and… I just can't be in that kind of relationship."

Teyla nodded to herself and then sighed. "I have long believed that love is a choice John, and that relationships of any kind require time and commitment. I do not know what your people believe on this matter, but you may find it helpful to keep in mind."

John glanced at her quickly and then looked forward again. Maybe she was right. Maybe he did have to choose to love Elizabeth. And they certainly hadn't put much time into their relationship recently. He was just sick of fighting and he didn't know if he could work up enough will power to overcome that barrier.

OOOOO

It had been almost two weeks since they'd had a conversation one on one that wasn't about work. The planet full of children had been an interesting experience last week but this week had been the real kicker. Weir had authorized the use of an experimental drug on a human and then authorized that it be tested on the wraith they had in the brig. It had succeeded in killing the wraith, but that was the problem. The people who had created the drug administered it to their entire population and it was only a matter of time before the wraith showed up at their door step to wipe them out. It was probably one of Atlatnis's greatest failures to date.

John sighed as he thought of all the events of the day, leaning over the balcony where he was standing and looking at the ocean. He felt responsible for the people's demise, as he knew did Carson, and that was a lot of people to be responsible for killing.

It was rare that John felt the inclination to cry. He had stopped crying when he was a boy, his father having indoctrinated in him the belief that real men don't cry. He still believed that, whether by choice or not, but felt an odd stinging in his eyes on this occasion. He pretended it was the wind but deep down he knew better. Keeping people safe was his job and if he had ever failed miserably, today was that day.

Hearing the door slide open behind him, he hurriedly rubbed his eyes and turned to see who it was, even though he already knew.

Weir allowed the door to shut behind her before she made her way slowly over to him.

"You okay?" She asked, even though she knew it was a dumb question.

He sighed and turned to look at the ocean again, crossing his arms. "No."

It came out flat, dead, like a deflated beach ball. She turned to look out at the sea as well.

"Me neither."

They stood there for a time, together in their grief and confusion. The stars twinkled above them, oblivious to their pain. Elizabeth felt tears begin to fall quietly and she allowed the night breeze to cool her wet face. After a while, John had still not moved from his position beside her and Elizabeth sighed, turning to go. There was nothing to say and it seemed John was not ready to embrace her.

As she turned, John put out a hand to stop her, grabbing her elbow gently. "Wait."

She turned back and he slid an arm around her waist, allowing her head to drop to his shoulder.

"I'm sorry I pushed you to let them test the drug. I shouldn't have. I was wrong."

Elizabeth shook her head on his shoulder. "No John, it wasn't your fault. We all wanted to test it. And the Hoffans wouldn't listen to reason."

Sighing, John placed his free hand on the railing. "Maybe… but I should have done something."

There was silence for a moment and then Elizabeth said quietly, "there was nothing we could have done."

They stood there, watching the waves, for a long time. Elizabeth felt the need to cry but couldn't bring herself to let the tears come. She was surprised when, sometime later, tears began falling from John's chin. Lifting her head and pulling away, she looked at his face. In all the years they had been married, John had only cried three times. It was one of the things Weir couldn't understand about him, one of the things that bothered her. Seeing his face so sad now melted her heart.

Putting her arms around him, she held him close, his face in her shoulder this time.

Maybe there was still hope for them. The fact that John was crying now gave her hope for the future. It was an odd emotion: happy he was crying yet sad for his pain. But, maybe he was changing. And maybe she was changing too. And maybe, just maybe, that meant their relationship could be renewed.


	5. Chapter 5

Chapter 5

Hello! Thanks to everyone who has been reading this story. It's been fun to write. I'm sorry it's been a while. I've recently started training to bike across the US next summer so that's taken up a lot of my free time. I will continue writing this story as I have time but, as is usually the case, between now and the holidays I'm going to be very busy, as I imagine many of you will be also. So, enjoy this chapter and thanks for reading! (And never fear, I'm not giving up on this story).

Their relationship had been acceptable of late. Though they continued to have disagreements, they also had good moments. It felt to Elizabeth as though their connection over the Hoffan drug problem had helped to break at least one small barrier between them. And, her complaint about John not being present wasn't true any longer. Living in the same city and working together every day did have its advantages.

And then came the epic storm, the one that almost wiped out Atlantis and took Elizabeth's life. That night, when John reflected on everything that had happened, he found it odd that he would be so affected by Elizabeth's death. It truly made him into a killing machine; the thought of never seeing her again. And the fact that someone else _chose _to take her from him made him even angrier. But he hadn't felt sadness at her loss, just deep rage, and he found that rather disconcerting.

Maybe there was no sadness because there wasn't time for it. Maybe he felt rage because of the nature of her death. He wondered if he felt rage because he still loved her or because he felt like she was _his_, and as such she was under his protection which meant he had failed in his duty.

After tossing and turning for hours that night, he finally got up and made his way resolutely to Elizabeth's room. For better or worse, he felt like he needed to be with her. He had almost lost her today, almost lost her to that monster Colya, and he needed to know she was still safe.

Ringing her bell he waited, expecting it to be a long wait, but it was only a short minute before she opened the door.

"John," she said in a slightly breathless voice. He rubbed his head awkwardly.

"Elizabeth, I just came by because-

He stopped when she wrapped her arms around him, feeling the strength and firmness of his body. He returned the gesture, finding it comforting to feel her heavy warmth between his arms. Pushing them into her room, he closed the door and the darkness of the night enfolded them. She was holding him so tightly he didn't think she would ever let go.

After a moment, he realized she was shaking and he kissed her on the head, taking one hand to run it through her hair. Pulling them to her bed, he sat down, pulling her with him. After a moment, Elizabeth seemed to realize that she was clinging to him and she sat up, releasing him and pushing the hair out of her face.

"I'm sorry, I'm just… it was a hard day that's all."

John almost laughed but touched her face with a hand. "Hey, a hard day is one in which three teams forget to check in and we have a fight about what beans to trade for. This day? This was like… Modern Warfare Atlantis."

Elizabeth snorted and rolled her eyes a little before looking down. "Yeah. I guess… when Colya was pulling me back towards the gate I didn't… I didn't know what would happen. I thought I would be their prisoner and I just…" She broke off as she took deep breaths. John reached forward to pull her in to his chest again and she breathed deeply of his familiar scent.

"I don't know what I was thinking when I thought you were dead," John began. "I guess I _wasn't _thinking. I was just trying to kill as many of his men as I could to avenge you and maybe get Atlantis back in the process."

He took a hand and started running it through her hair again.

"Come on," he said as he lay down on the bed, pulling her with him. "Let's sleep. And then we can leave this whole damn day behind us."

They lay silent for a moment but Elizabeth broke the silence soon after.

"John? Why did you feel like you needed to avenge me? You know that's not what I would want."

John lay in the darkness holding her, feeling her breathing against his chest. He thought for a moment and then shrugged.

"I don't know Elizabeth. I wasn't really doing much thinking. It was a combat situation and I did what I thought was necessary."

She was quiet for a long moment again and then she took a breath. "I understand that John, I really do, but if you really lose me, I don't want you to avenge me, not at the cost of human lives."

John sighed heavily, his grasp tightening around her. He could feel his jaw clenching slightly and he had to consciously focus on letting the tension go. Elizabeth wasn't a warrior, a fact he loved and hated about her. She always wanted to talk things through and didn't understand a soldier's mentality very well. It tended to be a big source of contention for them.

Not wanting to talk about it, John just closed his eyes and tried to slow his breathing, hoping she would let it go, but she wasn't so easily swayed. After a moment, she said,

"John, I know you're not asleep." Pushing herself up on her elbows, she looked at him through the darkness as his eyes opened. "Do you understand that my profession is all about defending human lives? How I fight with words so we don't have to fight with weapons?"

"Elizabeth…"

She cut him off. "Do you understand how avenging my death would be a total violation of the things I fight for?"

He fought the urge to roll his eyes and took a breath. "Elizabeth, I know that, you won't let me forget it. But what I did today? That wasn't just for you, that was for Atlantis and everyone who lives here. It was to defend Earth and to keep this city and all its knowledge from falling into the wrong hands."

"I know that John, and I'm not saying you did the wrong thing today-

"Really?" John cut her off as he pushed up on his elbows next to her. "Really? Because that's what it sounds like."

Elizabeth gave him one of her signature hard looks. "John, I support what you did today. If I had really died, I'm confident you would have saved Atlantis and everyone who lives here. I've just never seen you lose it like that and it… it scares me."

Looking at her murky form in front of him, he pressed his lips together. He really didn't want to talk about this and he wasn't interested in getting into a debate with her about vengeance. Because he knew that's what this would turn into.

"Elizabeth can we _please _just go to bed? I'm tired, it's been a long day, and I _really _don't want to debate the motives of my actions with you. I came here to make sure you were okay and comfort you if you needed it. Now can we please sleep?"

They looked at each other in the grayness of night and he could almost see Elizabeth fighting with herself. She knew if this were a negotiating situation, she would drop the subject and start in on something else, or she would approach the subject in a different way. But, since this was John, she felt like those rules didn't apply and, more often than not, found herself breaking her own rules of fighting and negotiating. It was always strange to her that it was easier to negotiate with strangers than it was with loved ones.

"John…" she said as she looked down and then plowed on despite her better judgment. "John I just want to make sure you're okay. I don't know if you realize how important it is to me that you _don't _do something like that again unless you have due cause, which admittedly you did this time."

That did it for John and he sat up, swinging his legs over the bed. "Elizabeth," he said as he stood. "I don't know if you were informed but, I'M A SOLDIER! This is what I do! And just so you know, my profession is ALSO about DEFENDING HUMAN LIVES. We just do it in different ways. And yes, I know, it's the same old argument we ALWAYS have. Well you know what? I'm sick of it!"

With one last look at her dark form, he made his way to the door and exited quickly before she could stop him.


	6. Chapter 6

Hello again! I just wanted to let you know that I skipped the episode "Hot Zone" because all the good scenes are pretty much already in it. It's kinda fun to watch that episode with this story line in mind though, so go try it! Thanks.

It had been a week since their most recent fight and they had been talking as little as possible. During that week, the city had endured a nano-virus outbreak, which almost everyone survived, but which sorely tested his and Elizabeth's relationship. The last thing Elizabeth had asked him after that hellish day was over had been, "do you trust me?" He had replied that he did, but he wondered how true that statement was. Everything that had happened that day had him questioning everything he felt about Elizabeth.

Rodney had noticed they were acting cooler towards each other than normal and had inquired about it, but John had brushed him off, doing his best to ignore him. Teyla was harder to ignore. She inquired about their relationship several times until John finally told her everything that had happened. After recounting the story, Teyla had very little to say except,

"Maybe you are not meant to be together then."

It almost sounded to John like she was being sarcastic, but he couldn't be sure. And then, to make matters worse, there was Chaia.

He was fairly smitten from the moment they set eyes on her; she was beautiful, kind, gentle, and especially responsive to him. He told himself that he and Dr. Weir were separated so he could do what he wanted, but he knew deep down that was a thinly veiled excuse. He didn't know why he was so taken with her, and he couldn't figure out why he'd let things progress so far; why he'd taken her to Atlantis or invited her to the pier with him. And then, to top things off, he ran into Teyla on his way to the pier. At first he thought she was going to be angry with him but she surprised him.

"_You are allowed to have feelings for others._"

He had tried to brush it off, pretending it was just a picnic to build relations between their two peoples but Teyla could see right through it.

"_Without having to justify them to anyone."_ She had said.

That surprised him most of all. He wondered if she was being sarcastic. Her little eyebrow raise when she said goodnight seemed to say a lot more than she had actually said, but he brushed it off. He knew what he was doing and he wasn't going to let her or anyone ruin his night.

And he did have a good time. The food was enjoyable, Chaia was great company, and kissing her just felt natural. After that, they quickly packed up the picnic and made their way towards Chaia's quarters. John could feel the tension growing in his chest as they got closer. He wanted to be with Chaia but he couldn't shake his damn conscience. If he did this, if he slept with her, he knew he would have to tell Elizabeth, and that would be the end. John knew he didn't want that.

Still, when they arrived, Chaia invited him in and he went, encouraging his brain to switch off, trying to focus on her brown eyes and smooth skin. She wasted no time, going in for a kiss and pulling him close to her. He allowed his hands to slide to her waste and she slid a hand behind his neck. She got as far as pushing off his jacket when he finally broke away. Taking a deep breath, he looked in her eyes.

"Chaia…" he paused as he saw the confusion in them. "I'm sorry, I can't do this."

She frowned. "Why not? I thought it did not bother you that I am an alien."

"No, it's not that at all." He took a moment to collect his thoughts and then plowed on. "I'm… Dr. Weir and I are married. Well, I mean, we're married but we're separated. We don't know if we want to be together any more… It's complicated." Seeing her face in confusion he added, "Life mates."

Then realization dawned. "You and Dr. Weir are life mates?"

John nodded and raised his eyebrows at the same time, expecting her to be angry. But she wasn't. She just nodded and walked a few steps away, thinking. After a moment she turned back.

"And you do not love each other anymore?"

John shrugged. "Like I said, it's complicated. But, I can't do this with you Chaia. I'm… I'm really sorry I led you on. It was wrong."

She sighed and smiled a little. "I led you on as much as you led me on. And… I enjoyed the time we spent together, even if it was… shorter than I would have liked."

Sighing, John reached down to get his jacket. When he straightened, he found Chaia in front of him again. She leaned up for a kiss and then smiled.

"If you change your mind, I'll still be here Major."

He nodded and pulled back, putting on his jacket again. "I'm sorry Chaia, I'll see you tomorrow."

After that, things had gotten weird. Rodney had caught him coming out of Chaia's bedroom. John had a sneaking suspicion he was going to tell Weir but he hoped his preoccupation with Chaia's alien presence would make him forget to tell her. Chaia, it turned out, was an Ancient, and had been banished to care for her planet. And Elizabeth, with all her powers of deduction, figured out that something was going on between John and Chaia.

When John left in the jumper, Elizabeth wondered if she would ever see him again. She had the odd feeling that even if he came back, he was lost to her forever. It was obvious at the meeting that morning that John and Chaia had been intimate, and Rodney's Kirk comment was not lost on her.

She opted to catch up on reports while she waited, trying not to think about what she would say to him when he got back. It surprised her that John would sleep with someone else while they were still married and she didn't know if she had anything left to say.

When he did finally arrive back, it was very late and only the graveyard shift was around. Elizabeth was dead to the world in a slump on her desk and didn't even hear the gate activate. Chuck rapped lightly on her door jam and she woke with a start.

"Sorry to wake you ma'am but Major Sheppard just arrived."

She nodded, trying to clear her head. "Thank you Chuck."

He left and she stared at the wall, trying to decide what to say. The truth was, she did care, deeply, that John had slept with Chaia. That told her a lot about how she felt about John. She did still love him. She did still care. She still wanted him all to herself. The fact that he had cheated on her cut her like a knife.

She decided to go to her quarters after that and to her surprise; John came to her door not long after she arrived. She answered it with hesitation, opening it to reveal his guilty face and crossed arms. Seeing his expression, she shook her head and was about to shut the door on him but he quickly jumped through the opening.

"Wait, Elizabeth." He placed a hand on her arm as the doors shut behind him. Sad tan eyes looked at him and he sighed.

"I'm sorry I ran off that way."

She continued to look at him, her expression unchanging.

"I… there's something I should tell you."

After a moment of silence, Elizabeth shrugged. "I already know you slept with her John."

She turned away quickly so he wouldn't see the tears that had formed in her eyes and began cleaning her room, for lack of anything better to do. She could feel John staring at her from his place by the door.

"And you don't care?" He asked. He could feel a knife turning in his own gut.

With her back to him, she shrugged. "No John, you can do what you want."

He could hear the anger in her voice, no matter how she tried to mask it, and he sighed internally, the pain easing a little.

"Well, for the record, I didn't."

Elizabeth paused and then turned, looking at him closely. "How can you say you didn't sleep with her? Rodney saw you coming out of her room! I know you had dinner on the pier. I just don't know why you feel the need to lie about it."

John sighed. "Elizabeth, I kissed her all right? That's what I wanted to tell you. I kissed her and we went to her room and I couldn't have sex with her because I was thinking about you. I knew it was wrong. So I told her everything and then I left."

As Elizabeth processed that information, John walked towards her. "She made me realize that I'm not ready to move on yet."

Elizabeth looked away from him as he continued to walk towards her. When he was standing before her, he took her hands in his and waited until she looked at him. He took a breath.

"Elizabeth… I know we have problems…" He paused for a moment. "I know that's putting it lightly… but I do still love you. That's obvious to me now." He paused trying to gauge her reaction and then continued. "Do you think… I mean, can we try to spend some time together? Like we used to? Maybe have breakfast or… go to the shooting range?"

The last comment almost got a smile from Elizabeth, but before it could take hold she pulled her hands away and turned from him. After a moment she turned back with a sigh and crossed her arms.

"John, I would love that, I really would, but I need to take it slow. The thing with you and Chaia? That really hurt me John and I just need time to think this through."

Her eyes were sad and he could see the tears sparkling at the rims. He swallowed hard and nodded, looking away.

"Yeah," he said, backing towards the door. "Sure. Just let me know when you want to catch up." He seemed unable to say anything else and left the room quickly. After he left, Elizabeth cried for a long time.


	7. Chapter 7

Episode text is in italics!

OOOOO

The day had dawned bright and clear, and Elizabeth had found herself on the balcony next to the control room, enjoying the fresh air. It was her birthday and she had wondered if John would find some way to give her a gift. As it turned out, he had remembered and he had even bought her the exact pot she had been wanting. How he found out, she would never know, but he was resourceful, she'd give him that.

He had left her alone on the balcony, only a moment ago, holding the beautiful pot he had purchased from the Athosians. She looked at it, smiling to herself. It had only been a few days since the Chaia incident and John had mostly kept his distance except for work, which Elizabeth appreciated. But this thoughtful gift meant a lot to her, especially since one of their last arguments before separating had been about forgetting important dates.

She smiled to herself. It seemed Atlantis was changing him.

OOOOO

Several hours later, they had found the ancient Dr. Weir in a pod in a room they had not yet explored. She had been able to tell them part of her story, but had not yet made it through the whole thing. The young Dr. Weir had gone back to her office to do some work with explicit instructions to contact her if Old Weir woke up again. John was on watch duty.

Since it was nearing the time of night when everyone else was asleep, John was hoping he would be alone with Weir. He wanted to ask her some questions about their relationship without anyone else listening in.

He had almost fallen asleep when he heard a feeble voice say,

"John?"

He picked up his head from the bed quickly and blinked, trying to clear his vision. After a moment, he smiled at the old woman.

"Hey, how are you feeling?"

She smiled with dancing eyes. "Oh you know… old."

John laughed lightly and leaned back in his chair, looking at her and wondering if he should turn off the recording device that was always trained on Old Weir.

_No,_ he thought to himself, _she might say something important and then where will I be? In the dog house with my Weir, that's for sure._

Old Weir was looking at him with knowing eyes but she was waiting for him to start the conversation. He cleared his throat awkwardly.

"So," he began, "It's your birthday today."

A smile opened on her face. "Ah, so it is! And how old am I today?"

John smiled. "You'll be 36."

Old Weir laughed softly. "So young! So you must be coming up on 38 then." Her eyes were twinkling.

"Yeah, you never could let that go could you?"

Her crackly laugh came out again. "No, I suppose not."

He cleared his throat and crossed his arms against his chest. "So, that means… we were married?"

She smiled at him and nodded, tears coming to her eyes as she took in his features. "Yes, we were."

"And separated?"

She looked at him and nodded again.

He looked down and fiddled with his jacket, wondering what to say next. Old Weir reached out a hand and took one of John's, pulling it up to the bed. He looked up at her and saw the tears that were now tracing lines down her face.

"John," she said, "I know we had… have… issues. But let me tell you from someone who knows… life is quick." She paused for a moment and then continued. "Even though I separated from you, I still love you. When you died in that puddle jumper… when Jonas told me no one else had survived… losing you was one of the hardest things I've ever had to endure."

John tightened his lips and awkwardly cleared his throat, trying to blink away the wetness that was entering his eyes. Old Weir took a breath, her voice more strained than before.

"John, take it from me… I want to be with you again. I'm just scared that I'll be hurt and let down like I was before."

John nodded, flicking his eyes up at her and then looking down again. He had hurt Elizabeth. They had hurt each other. And John knew if they were going to try this again, some things would have to be different.

"You think there's hope for us?" He asked, looking up and taking in Elizabeth's old features. She smiled slightly through the tears that were in her eyes.

"Yes, John, I do. I asked you to come on the mission _because _I still had hope. I wasn't ready to let you go. And I think you came along because you felt the same."

He nodded slightly and she continued.

"Things were hard that last year before we separated. But things are different here!" she said earnestly. "Atlantis is like a new start for us, a new place, a new life. If you're willing, we can get back to how we used to be."

John let out a short, quiet laugh that indicated his disbelief. "I don't know if we'll _ever _get back to how we _used _to be."

Elizabeth sighed and looked at him patiently. "The question you have to ask yourself is, do you think your relationship with me is more important than your stubbornness and pride? And yes, John Sheppherd, you have stubbornness in spades!"

"Well," John said, getting annoyed despite himself, "so do you!"

They stared at each other for a long moment, Weir's hand tight around his, and then she smiled and shook her head, laughing quietly.

"Even after 10,000 years we can still manage to fight."

John looked aside sheepishly and rubbed his head with his free hand.

"John," she said, her voice weak, "I gave my life so we could have a second chance, so Atlantis could have a second chance. Life is quick… don't waste it."

He looked into her eyes; his brow furrowed, and felt Weir's hand relax on his. She had fallen asleep again.

OOOOO

It was some time later. John and Rodney were both conked out behind her and Elizabeth was talking to the old version of herself, who had just woken.

"_I'm just saying stop being so damn hard on yourself." Old Weir was saying. "Life is quick"_

_Elizabeth smiled sadly. "Not for you."_

"_It was my choice Elizabeth. I didn't second guess it then. And I don't regret it now."_

They looked at each other for a long moment and then Old Weir took a breath. "Elizabeth, John and I were married in my time too."

Surprised at the change of subject, Elizabeth raised her eyebrows and then glanced carefully behind her to make sure John was still sleeping. When she turned back, Old Weir had a knowing smile on her lips.

"You still love him, Elizabeth."

Holding her eyes for a moment, she nodded. "Yes, of course I do."

"Then give him another chance." Her eyes were earnest and they flicked briefly to John's sleeping form.

Young Elizabeth looked down at her hands and paused for a moment, thinking. "I'm just afraid of being hurt again. I'm afraid of hoping for more from our relationship and getting exactly what I left back on Earth. I'm afraid…" she looked up. "I'm afraid we'll fall back into old habits."

Old Weir nodded with understanding. "I know. I know that fear better than anyone else because I felt it too. But the reason you asked him to come to Atlantis is because you wanted to give him a second chance." She paused, looking into her hazel eyes. "Do what you have to, see Dr. Heitmeier, but give it a chance Elizabeth. Fear is never a good reason to avoid something… life is quick."

They looked into each other's eyes, each looking into another version of themselves. Then finally, after a long moment, Old Weir continued telling her story.

OOOOO

She was dead.

The old version of herself had died, as was expected, but it still came as a shock to Elizabeth. It was strange, seeing herself die, and made her very aware of her own mortality.

"_Trust yourself Elizabeth,"_ Old Weir had said with knowing eyes, "_All that matters is right now."_

An understanding look passed between them and they had both known she was talking about John and her relationship.

Sighing, Elizabeth opened the jar that John had given her and let the ashes of her other self fall to the wind. Watching them blow away, she was overcome with emotion and realized that, if nothing else, she had to give John a second chance to honor Old Weir's memory. Her journey, her life, her lack of a life, had all been to give them all a second chance. And, when it came down to it, she was right, life was quick.

Later that day, they were exiting the mission briefing and Weir jogged to catch up with Sheppherd.

"John," she said as she came up behind him. He turned towards her in surprise and gave her a tight smile.

"What's up?"

The expression on his face was almost eager and Elizabeth had to smile. It reminded her of the John she knew so many years ago. He stopped walking just shy of the stairs and gave her a questioning look.

"What?"

"Oh, nothing. It's just, you reminded me of your young, carefree self for a moment."

He didn't know what to say for a beat and then replied, "Well, maybe he's making a comeback."

Weir smiled and then looked down, taking a breath to calm her fluttering stomach.

"John," she said, looking up, "would you like to have lunch today? With me? I mean… like we used to."

John could feel little tingles of excitement spreading through his veins at her question. It was almost like it was a new relationship and she was asking him out for the first time. He gave her one of his signature cocky smiles.

"Dr. Weir, I would be honored."


End file.
